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Establishment and analysis of a reference transcriptome for Spodoptera frugiperda.

Legeai F, Gimenez S, Duvic B, Escoubas JM, Gosselin Grenet AS, Blanc F, Cousserans F, Séninet I, Bretaudeau A, Mutuel D, Girard PA, Monsempes C, Magdelenat G, Hilliou F, Feyereisen R, Ogliastro M, Volkoff AN, Jacquin-Joly E, d'Alençon E, Nègre N, Fournier P - BMC Genomics (2014)

Bottom Line: We conclude that the Sf_TR2012b transcriptome is a valid reference transcriptome.While its reliability decreases for the detection and annotation of genes under strong transcriptional constraint we still recover a fair percentage of tissue-specific transcripts.Similarly, we observed an interesting interplay of gene families involved in immunity between fat bodies and antennae.

View Article: PubMed Central - PubMed

Affiliation: INRA, UMR1333, DGIMI, Montpellier, France. nicolas.negre@univ-montp2.fr.

ABSTRACT

Background: Spodoptera frugiperda (Noctuidae) is a major agricultural pest throughout the American continent. The highly polyphagous larvae are frequently devastating crops of importance such as corn, sorghum, cotton and grass. In addition, the Sf9 cell line, widely used in biochemistry for in vitro protein production, is derived from S. frugiperda tissues. Many research groups are using S. frugiperda as a model organism to investigate questions such as plant adaptation, pest behavior or resistance to pesticides.

Results: In this study, we constructed a reference transcriptome assembly (Sf_TR2012b) of RNA sequences obtained from more than 35 S. frugiperda developmental time-points and tissue samples. We assessed the quality of this reference transcriptome by annotating a ubiquitous gene family--ribosomal proteins--as well as gene families that have a more constrained spatio-temporal expression and are involved in development, immunity and olfaction. We also provide a time-course of expression that we used to characterize the transcriptional regulation of the gene families studied.

Conclusion: We conclude that the Sf_TR2012b transcriptome is a valid reference transcriptome. While its reliability decreases for the detection and annotation of genes under strong transcriptional constraint we still recover a fair percentage of tissue-specific transcripts. That allowed us to explore the spatial and temporal expression of genes and to observe that some olfactory receptors are expressed in antennae and palps but also in other non related tissues such as fat bodies. Similarly, we observed an interesting interplay of gene families involved in immunity between fat bodies and antennae.

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Related in: MedlinePlus

Representation of transcripts and their expression. A. Screenshot of the GBrowse system integrated in the Lepidodb. A region centered around spod-11-tox [34] is represented on the 33K20_Sf BAC. The manual annotation of this already described gene can be compared with KAIKOGASS_mRNA predictions (top track) and Sf_TR2012b transcript (second to top track). The bottom two tracks represent coverage reads from 2 Illumina tissue RNAseq experiments, induced fat bodies and larval antennae and palps. B. Venn diagram showing the overlap between Kaikogass gene predictions on the BACS and Sf_TR2012b transcripts aligned on the same BACs. C. Correlogram of the rpm values for each of the developmental time points and tissue RNAseq experiments.
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Fig3: Representation of transcripts and their expression. A. Screenshot of the GBrowse system integrated in the Lepidodb. A region centered around spod-11-tox [34] is represented on the 33K20_Sf BAC. The manual annotation of this already described gene can be compared with KAIKOGASS_mRNA predictions (top track) and Sf_TR2012b transcript (second to top track). The bottom two tracks represent coverage reads from 2 Illumina tissue RNAseq experiments, induced fat bodies and larval antennae and palps. B. Venn diagram showing the overlap between Kaikogass gene predictions on the BACS and Sf_TR2012b transcripts aligned on the same BACs. C. Correlogram of the rpm values for each of the developmental time points and tissue RNAseq experiments.

Mentions: The Sf_TR2012b assembly sequences can be downloaded through the Lepidodb database (http://www6.inra.fr/lepidodb/Private and http://www.inra.fr/lepidodb/downloads/TR2012b) [login: lepiduser password: papillon]. In this database, the transcripts can be queried with their identifier or with the name of an ortholog. BLASTx against the nr database have been performed for all transcripts in the assembly and the database contain the best 10 results for each transcript. BLAST searches can also be performed from the database. In addition a GBrowse system has been added that presents a set 44 BAC sequences (25 BAC sequences have been added in LepidoDB to the 19 already published [31]) representing each around 100 kb of contiguous genomic sequence, on which a computed gene prediction has been performed by KAIKOGAAS (http://kaikogaas.dna.affrc.go.jp/). We aligned the Sf_TR2012b transcripts on this genomic reference [31]. The alignment results by blast have been converted into a .gff3 file directly viewable in a GBrowse genomic viewer instance [32] hosted through the Lepidodb portal (http://www6.inra.fr/lepidodb/Private) (Figure 3A). Throughout the BACs, we have 49.4% of KAIKOGAAS gene predictions that overlap with an Sf_TR2012b transcript, while 80.3% of Sf_TR2012b overlap with a gene prediction (Figure 3B). We also provide for each transcript its level of expression for 10 different samples. These levels of expression are also represented on the BACs present in LepidoDB as tracks (Figure 3A) [33].Figure 3


Establishment and analysis of a reference transcriptome for Spodoptera frugiperda.

Legeai F, Gimenez S, Duvic B, Escoubas JM, Gosselin Grenet AS, Blanc F, Cousserans F, Séninet I, Bretaudeau A, Mutuel D, Girard PA, Monsempes C, Magdelenat G, Hilliou F, Feyereisen R, Ogliastro M, Volkoff AN, Jacquin-Joly E, d'Alençon E, Nègre N, Fournier P - BMC Genomics (2014)

Representation of transcripts and their expression. A. Screenshot of the GBrowse system integrated in the Lepidodb. A region centered around spod-11-tox [34] is represented on the 33K20_Sf BAC. The manual annotation of this already described gene can be compared with KAIKOGASS_mRNA predictions (top track) and Sf_TR2012b transcript (second to top track). The bottom two tracks represent coverage reads from 2 Illumina tissue RNAseq experiments, induced fat bodies and larval antennae and palps. B. Venn diagram showing the overlap between Kaikogass gene predictions on the BACS and Sf_TR2012b transcripts aligned on the same BACs. C. Correlogram of the rpm values for each of the developmental time points and tissue RNAseq experiments.
© Copyright Policy - open-access
Related In: Results  -  Collection

License 1 - License 2
Show All Figures
getmorefigures.php?uid=PMC4150953&req=5

Fig3: Representation of transcripts and their expression. A. Screenshot of the GBrowse system integrated in the Lepidodb. A region centered around spod-11-tox [34] is represented on the 33K20_Sf BAC. The manual annotation of this already described gene can be compared with KAIKOGASS_mRNA predictions (top track) and Sf_TR2012b transcript (second to top track). The bottom two tracks represent coverage reads from 2 Illumina tissue RNAseq experiments, induced fat bodies and larval antennae and palps. B. Venn diagram showing the overlap between Kaikogass gene predictions on the BACS and Sf_TR2012b transcripts aligned on the same BACs. C. Correlogram of the rpm values for each of the developmental time points and tissue RNAseq experiments.
Mentions: The Sf_TR2012b assembly sequences can be downloaded through the Lepidodb database (http://www6.inra.fr/lepidodb/Private and http://www.inra.fr/lepidodb/downloads/TR2012b) [login: lepiduser password: papillon]. In this database, the transcripts can be queried with their identifier or with the name of an ortholog. BLASTx against the nr database have been performed for all transcripts in the assembly and the database contain the best 10 results for each transcript. BLAST searches can also be performed from the database. In addition a GBrowse system has been added that presents a set 44 BAC sequences (25 BAC sequences have been added in LepidoDB to the 19 already published [31]) representing each around 100 kb of contiguous genomic sequence, on which a computed gene prediction has been performed by KAIKOGAAS (http://kaikogaas.dna.affrc.go.jp/). We aligned the Sf_TR2012b transcripts on this genomic reference [31]. The alignment results by blast have been converted into a .gff3 file directly viewable in a GBrowse genomic viewer instance [32] hosted through the Lepidodb portal (http://www6.inra.fr/lepidodb/Private) (Figure 3A). Throughout the BACs, we have 49.4% of KAIKOGAAS gene predictions that overlap with an Sf_TR2012b transcript, while 80.3% of Sf_TR2012b overlap with a gene prediction (Figure 3B). We also provide for each transcript its level of expression for 10 different samples. These levels of expression are also represented on the BACs present in LepidoDB as tracks (Figure 3A) [33].Figure 3

Bottom Line: We conclude that the Sf_TR2012b transcriptome is a valid reference transcriptome.While its reliability decreases for the detection and annotation of genes under strong transcriptional constraint we still recover a fair percentage of tissue-specific transcripts.Similarly, we observed an interesting interplay of gene families involved in immunity between fat bodies and antennae.

View Article: PubMed Central - PubMed

Affiliation: INRA, UMR1333, DGIMI, Montpellier, France. nicolas.negre@univ-montp2.fr.

ABSTRACT

Background: Spodoptera frugiperda (Noctuidae) is a major agricultural pest throughout the American continent. The highly polyphagous larvae are frequently devastating crops of importance such as corn, sorghum, cotton and grass. In addition, the Sf9 cell line, widely used in biochemistry for in vitro protein production, is derived from S. frugiperda tissues. Many research groups are using S. frugiperda as a model organism to investigate questions such as plant adaptation, pest behavior or resistance to pesticides.

Results: In this study, we constructed a reference transcriptome assembly (Sf_TR2012b) of RNA sequences obtained from more than 35 S. frugiperda developmental time-points and tissue samples. We assessed the quality of this reference transcriptome by annotating a ubiquitous gene family--ribosomal proteins--as well as gene families that have a more constrained spatio-temporal expression and are involved in development, immunity and olfaction. We also provide a time-course of expression that we used to characterize the transcriptional regulation of the gene families studied.

Conclusion: We conclude that the Sf_TR2012b transcriptome is a valid reference transcriptome. While its reliability decreases for the detection and annotation of genes under strong transcriptional constraint we still recover a fair percentage of tissue-specific transcripts. That allowed us to explore the spatial and temporal expression of genes and to observe that some olfactory receptors are expressed in antennae and palps but also in other non related tissues such as fat bodies. Similarly, we observed an interesting interplay of gene families involved in immunity between fat bodies and antennae.

Show MeSH
Related in: MedlinePlus